Multiple sequence alignment - TraesCS6D01G381300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G381300 chr6D 100.000 5568 0 0 1 5568 461716900 461711333 0.000000e+00 10283.0
1 TraesCS6D01G381300 chr6B 93.884 3597 137 44 1520 5065 704041963 704038399 0.000000e+00 5347.0
2 TraesCS6D01G381300 chr6B 89.385 829 46 22 610 1407 704042875 704042058 0.000000e+00 1005.0
3 TraesCS6D01G381300 chr6B 86.971 307 35 3 5203 5509 704038358 704038057 1.920000e-89 340.0
4 TraesCS6D01G381300 chr6B 87.815 238 9 11 142 359 704043660 704043423 1.540000e-65 261.0
5 TraesCS6D01G381300 chr6B 87.895 190 23 0 5267 5456 704035133 704034944 2.020000e-54 224.0
6 TraesCS6D01G381300 chr6B 97.468 79 2 0 420 498 704042972 704042894 9.730000e-28 135.0
7 TraesCS6D01G381300 chr6A 94.742 1997 61 23 1455 3435 608633887 608631919 0.000000e+00 3066.0
8 TraesCS6D01G381300 chr6A 93.654 1765 70 21 3837 5568 608631427 608629672 0.000000e+00 2601.0
9 TraesCS6D01G381300 chr6A 92.245 1354 58 23 138 1461 608635248 608633912 0.000000e+00 1875.0
10 TraesCS6D01G381300 chr6A 83.019 477 39 24 3379 3844 608631923 608631478 1.450000e-105 394.0
11 TraesCS6D01G381300 chr6A 95.070 142 6 1 2 142 79122578 79122437 7.260000e-54 222.0
12 TraesCS6D01G381300 chr6A 81.720 93 14 3 1678 1769 608633474 608633384 2.150000e-09 75.0
13 TraesCS6D01G381300 chrUn 97.080 137 4 0 2 138 230804497 230804633 1.210000e-56 231.0
14 TraesCS6D01G381300 chrUn 97.080 137 4 0 2 138 410917173 410917309 1.210000e-56 231.0
15 TraesCS6D01G381300 chr4D 97.080 137 3 1 2 138 42146142 42146277 4.340000e-56 230.0
16 TraesCS6D01G381300 chr1D 96.429 140 3 2 2 139 326967707 326967568 4.340000e-56 230.0
17 TraesCS6D01G381300 chr1D 96.403 139 3 2 2 138 20542735 20542873 1.560000e-55 228.0
18 TraesCS6D01G381300 chr7D 96.377 138 4 1 2 138 151776354 151776217 5.610000e-55 226.0
19 TraesCS6D01G381300 chr3A 95.714 140 4 2 2 139 1518386 1518525 2.020000e-54 224.0
20 TraesCS6D01G381300 chr2D 94.521 146 5 3 2 145 308103953 308104097 7.260000e-54 222.0
21 TraesCS6D01G381300 chr2D 95.000 40 1 1 2265 2304 29873787 29873749 1.670000e-05 62.1
22 TraesCS6D01G381300 chr3B 95.349 43 2 0 2262 2304 793014182 793014224 1.000000e-07 69.4
23 TraesCS6D01G381300 chr5D 91.837 49 3 1 1623 1671 490450272 490450319 3.600000e-07 67.6
24 TraesCS6D01G381300 chr7B 95.000 40 1 1 2265 2304 321386621 321386659 1.670000e-05 62.1
25 TraesCS6D01G381300 chr2A 93.023 43 2 1 2262 2304 203195061 203195102 1.670000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G381300 chr6D 461711333 461716900 5567 True 10283.000000 10283 100.000000 1 5568 1 chr6D.!!$R1 5567
1 TraesCS6D01G381300 chr6B 704034944 704043660 8716 True 1218.666667 5347 90.569667 142 5509 6 chr6B.!!$R1 5367
2 TraesCS6D01G381300 chr6A 608629672 608635248 5576 True 1602.200000 3066 89.076000 138 5568 5 chr6A.!!$R2 5430

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
380 417 0.119155 AGTGAGAAGGACATGGGGGA 59.881 55.000 0.00 0.00 0.00 4.81 F
1856 2381 0.307453 TTGTGCACAGCTGTAAAGCG 59.693 50.000 21.20 7.99 40.27 4.68 F
2013 2550 0.465705 CATCCCTCGCCATGTACAGT 59.534 55.000 0.33 0.00 0.00 3.55 F
2541 3079 1.889829 GGTGGATATCCTCCTCAGTCG 59.110 57.143 28.43 0.00 45.21 4.18 F
3674 4267 0.178967 TGGCTGCAATTCCCAGAACA 60.179 50.000 0.50 2.85 32.03 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2516 1.111715 GGATGCCAATTCTCCAGCCC 61.112 60.000 0.00 0.0 0.00 5.19 R
3124 3662 0.456221 ACTCGTAGCCATCCTCAACG 59.544 55.000 0.00 0.0 34.99 4.10 R
3657 4250 1.251251 AGTGTTCTGGGAATTGCAGC 58.749 50.000 0.00 0.0 0.00 5.25 R
3689 4282 1.770658 TCAAGTGCATGGGAGATAGGG 59.229 52.381 0.00 0.0 0.00 3.53 R
5070 5762 1.926665 AGGCCACCACCCAATAACATA 59.073 47.619 5.01 0.0 0.00 2.29 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.603963 TGATTTCATGATGAATTTTTGCAGG 57.396 32.000 8.90 0.00 36.11 4.85
26 27 5.866335 TTTCATGATGAATTTTTGCAGGC 57.134 34.783 8.90 0.00 36.11 4.85
27 28 4.538746 TCATGATGAATTTTTGCAGGCA 57.461 36.364 0.00 0.00 0.00 4.75
28 29 4.247258 TCATGATGAATTTTTGCAGGCAC 58.753 39.130 0.00 0.00 0.00 5.01
29 30 4.020928 TCATGATGAATTTTTGCAGGCACT 60.021 37.500 0.00 0.00 43.88 4.40
30 31 4.339872 TGATGAATTTTTGCAGGCACTT 57.660 36.364 0.00 0.00 34.60 3.16
31 32 5.465532 TGATGAATTTTTGCAGGCACTTA 57.534 34.783 0.00 0.00 34.60 2.24
32 33 5.472148 TGATGAATTTTTGCAGGCACTTAG 58.528 37.500 0.00 0.00 34.60 2.18
33 34 5.243507 TGATGAATTTTTGCAGGCACTTAGA 59.756 36.000 0.00 0.00 34.60 2.10
34 35 5.528043 TGAATTTTTGCAGGCACTTAGAA 57.472 34.783 0.00 0.00 34.60 2.10
35 36 5.288804 TGAATTTTTGCAGGCACTTAGAAC 58.711 37.500 0.00 0.00 34.60 3.01
36 37 5.068987 TGAATTTTTGCAGGCACTTAGAACT 59.931 36.000 0.00 0.00 34.60 3.01
37 38 5.535753 ATTTTTGCAGGCACTTAGAACTT 57.464 34.783 0.00 0.00 34.60 2.66
38 39 5.337578 TTTTTGCAGGCACTTAGAACTTT 57.662 34.783 0.00 0.00 34.60 2.66
39 40 5.337578 TTTTGCAGGCACTTAGAACTTTT 57.662 34.783 0.00 0.00 34.60 2.27
40 41 3.988379 TGCAGGCACTTAGAACTTTTG 57.012 42.857 0.00 0.00 34.60 2.44
41 42 3.287222 TGCAGGCACTTAGAACTTTTGT 58.713 40.909 0.00 0.00 34.60 2.83
42 43 3.315191 TGCAGGCACTTAGAACTTTTGTC 59.685 43.478 0.00 0.00 34.60 3.18
43 44 3.315191 GCAGGCACTTAGAACTTTTGTCA 59.685 43.478 0.00 0.00 34.60 3.58
44 45 4.202010 GCAGGCACTTAGAACTTTTGTCAA 60.202 41.667 0.00 0.00 34.60 3.18
45 46 5.507985 GCAGGCACTTAGAACTTTTGTCAAT 60.508 40.000 0.00 0.00 34.60 2.57
46 47 5.916883 CAGGCACTTAGAACTTTTGTCAATG 59.083 40.000 0.00 0.00 34.60 2.82
47 48 5.594317 AGGCACTTAGAACTTTTGTCAATGT 59.406 36.000 0.00 0.00 27.25 2.71
48 49 6.096846 AGGCACTTAGAACTTTTGTCAATGTT 59.903 34.615 4.72 4.72 27.25 2.71
49 50 6.756542 GGCACTTAGAACTTTTGTCAATGTTT 59.243 34.615 6.10 0.00 31.96 2.83
50 51 7.043391 GGCACTTAGAACTTTTGTCAATGTTTC 60.043 37.037 6.10 1.04 31.96 2.78
51 52 7.702348 GCACTTAGAACTTTTGTCAATGTTTCT 59.298 33.333 6.10 6.96 31.96 2.52
52 53 9.226345 CACTTAGAACTTTTGTCAATGTTTCTC 57.774 33.333 6.42 0.00 31.96 2.87
53 54 9.178758 ACTTAGAACTTTTGTCAATGTTTCTCT 57.821 29.630 6.42 3.36 31.96 3.10
54 55 9.657121 CTTAGAACTTTTGTCAATGTTTCTCTC 57.343 33.333 6.42 0.00 31.96 3.20
55 56 7.630242 AGAACTTTTGTCAATGTTTCTCTCA 57.370 32.000 6.10 0.00 31.96 3.27
56 57 8.055279 AGAACTTTTGTCAATGTTTCTCTCAA 57.945 30.769 6.10 0.00 31.96 3.02
57 58 8.522830 AGAACTTTTGTCAATGTTTCTCTCAAA 58.477 29.630 6.10 0.00 31.96 2.69
58 59 9.139174 GAACTTTTGTCAATGTTTCTCTCAAAA 57.861 29.630 6.10 0.00 31.96 2.44
59 60 9.487790 AACTTTTGTCAATGTTTCTCTCAAAAA 57.512 25.926 0.00 0.00 34.51 1.94
102 103 5.987777 TTTTCGATTTTACTGTTCACCGA 57.012 34.783 0.00 0.00 0.00 4.69
103 104 5.585500 TTTCGATTTTACTGTTCACCGAG 57.415 39.130 0.00 0.00 0.00 4.63
104 105 2.991190 TCGATTTTACTGTTCACCGAGC 59.009 45.455 0.00 0.00 0.00 5.03
105 106 2.993899 CGATTTTACTGTTCACCGAGCT 59.006 45.455 0.00 0.00 0.00 4.09
106 107 3.060895 CGATTTTACTGTTCACCGAGCTC 59.939 47.826 2.73 2.73 0.00 4.09
107 108 3.462483 TTTTACTGTTCACCGAGCTCA 57.538 42.857 15.40 0.00 0.00 4.26
108 109 3.462483 TTTACTGTTCACCGAGCTCAA 57.538 42.857 15.40 0.00 0.00 3.02
109 110 3.462483 TTACTGTTCACCGAGCTCAAA 57.538 42.857 15.40 0.00 0.00 2.69
110 111 2.550830 ACTGTTCACCGAGCTCAAAT 57.449 45.000 15.40 0.00 0.00 2.32
111 112 2.146342 ACTGTTCACCGAGCTCAAATG 58.854 47.619 15.40 8.47 0.00 2.32
112 113 2.224281 ACTGTTCACCGAGCTCAAATGA 60.224 45.455 15.40 10.78 0.00 2.57
113 114 2.414481 CTGTTCACCGAGCTCAAATGAG 59.586 50.000 15.40 6.05 44.75 2.90
131 132 2.665000 CTCGGGAGCAGAAAGGCA 59.335 61.111 0.00 0.00 35.83 4.75
132 133 1.743252 CTCGGGAGCAGAAAGGCAC 60.743 63.158 0.00 0.00 35.83 5.01
225 243 9.500785 CAAGAAGAATAAGAAGAAAAGGTCTCT 57.499 33.333 0.00 0.00 34.56 3.10
291 324 4.099113 CACTTCACAGGCTCTCATCATCTA 59.901 45.833 0.00 0.00 0.00 1.98
366 403 6.030548 TCTGACTAGGAAATGTCAAGTGAG 57.969 41.667 0.00 0.00 41.80 3.51
380 417 0.119155 AGTGAGAAGGACATGGGGGA 59.881 55.000 0.00 0.00 0.00 4.81
381 418 0.543749 GTGAGAAGGACATGGGGGAG 59.456 60.000 0.00 0.00 0.00 4.30
383 420 1.988982 GAGAAGGACATGGGGGAGCC 61.989 65.000 0.00 0.00 0.00 4.70
385 422 1.856873 AAGGACATGGGGGAGCCAA 60.857 57.895 0.00 0.00 0.00 4.52
387 424 1.380380 GGACATGGGGGAGCCAAAG 60.380 63.158 0.00 0.00 0.00 2.77
409 446 2.093764 CACTTTGCAGAAACAACCCCAA 60.094 45.455 0.00 0.00 0.00 4.12
552 979 3.239449 TGGCACAAGGAGAGAGAAAGTA 58.761 45.455 0.00 0.00 31.92 2.24
576 1003 4.651503 ACAGAGAGAGGTAGAGAGAGAGAG 59.348 50.000 0.00 0.00 0.00 3.20
577 1004 4.039730 CAGAGAGAGGTAGAGAGAGAGAGG 59.960 54.167 0.00 0.00 0.00 3.69
642 1069 4.222588 ACAAGAAGAGATCAGTGAGAAGGG 59.777 45.833 0.00 0.00 0.00 3.95
685 1112 0.544697 AGAGGAGAGGAGACGAGACC 59.455 60.000 0.00 0.00 0.00 3.85
750 1177 1.153229 ACGAGGGAATAAAGCGGCC 60.153 57.895 0.00 0.00 0.00 6.13
910 1355 5.010012 TCTGTGCTTGATTCCTTTCCTTTTC 59.990 40.000 0.00 0.00 0.00 2.29
948 1395 7.309177 GGGATAGCTTTGTTTTCTTCTTCTTC 58.691 38.462 0.00 0.00 0.00 2.87
950 1397 8.572185 GGATAGCTTTGTTTTCTTCTTCTTCTT 58.428 33.333 0.00 0.00 0.00 2.52
989 1439 5.447573 GTTGTTGAGAAGCTCTTGATTGAC 58.552 41.667 0.00 0.00 0.00 3.18
1206 1659 1.484444 CCCCTCCCTCGATTCATCCC 61.484 65.000 0.00 0.00 0.00 3.85
1363 1819 1.608590 CTGCAGTAGCTCTCCTCTAGC 59.391 57.143 5.25 0.00 42.74 3.42
1372 1828 2.360801 GCTCTCCTCTAGCGATTTCAGT 59.639 50.000 0.00 0.00 0.00 3.41
1518 2035 5.585390 CAAGGTACTCATCCAATTGAATGC 58.415 41.667 7.12 0.00 38.49 3.56
1603 2120 4.023193 GCTTGCTAAGTTTTAGGTGCTTCA 60.023 41.667 0.00 0.00 0.00 3.02
1631 2148 5.833131 TCTGACAAAAGGCCAGATTTAGTTT 59.167 36.000 5.01 0.00 32.57 2.66
1719 2240 2.778299 TGATTGACTTTTGGAGACCCG 58.222 47.619 0.00 0.00 34.29 5.28
1817 2338 5.684704 TGATTAGCTTTGGAGAACCATAGG 58.315 41.667 0.00 0.00 46.34 2.57
1856 2381 0.307453 TTGTGCACAGCTGTAAAGCG 59.693 50.000 21.20 7.99 40.27 4.68
1943 2480 4.747540 TGCACAGTTGTAAAGCAGTATG 57.252 40.909 0.00 0.00 40.87 2.39
1979 2516 5.106673 GGCTTGCTTTGGTAGTTAACTGTAG 60.107 44.000 18.56 8.68 0.00 2.74
2010 2547 4.049393 GCATCCCTCGCCATGTAC 57.951 61.111 0.00 0.00 0.00 2.90
2012 2549 0.882042 GCATCCCTCGCCATGTACAG 60.882 60.000 0.33 0.00 0.00 2.74
2013 2550 0.465705 CATCCCTCGCCATGTACAGT 59.534 55.000 0.33 0.00 0.00 3.55
2015 2552 2.082140 TCCCTCGCCATGTACAGTAT 57.918 50.000 0.33 0.00 0.00 2.12
2017 2554 3.774734 TCCCTCGCCATGTACAGTATAT 58.225 45.455 0.33 0.00 0.00 0.86
2018 2555 4.925836 TCCCTCGCCATGTACAGTATATA 58.074 43.478 0.33 0.00 0.00 0.86
2019 2556 5.326900 TCCCTCGCCATGTACAGTATATAA 58.673 41.667 0.33 0.00 0.00 0.98
2020 2557 5.417894 TCCCTCGCCATGTACAGTATATAAG 59.582 44.000 0.33 0.00 0.00 1.73
2021 2558 5.417894 CCCTCGCCATGTACAGTATATAAGA 59.582 44.000 0.33 0.00 0.00 2.10
2022 2559 6.404844 CCCTCGCCATGTACAGTATATAAGAG 60.405 46.154 0.33 2.45 0.00 2.85
2023 2560 5.950883 TCGCCATGTACAGTATATAAGAGC 58.049 41.667 0.33 0.00 0.00 4.09
2205 2742 5.237344 GCAATGGTTGTGTATATCAGGTCTC 59.763 44.000 0.00 0.00 0.00 3.36
2222 2759 9.911788 ATCAGGTCTCTGTGTCATTTTATTTAT 57.088 29.630 0.00 0.00 41.59 1.40
2541 3079 1.889829 GGTGGATATCCTCCTCAGTCG 59.110 57.143 28.43 0.00 45.21 4.18
2794 3332 7.615582 TCAGCGTTGATAGATGAAAAGATTT 57.384 32.000 0.00 0.00 30.51 2.17
3073 3611 6.678568 AAACACCCATCACATTATTTTCCA 57.321 33.333 0.00 0.00 0.00 3.53
3124 3662 4.090761 TCTGCATATTGGAATCCAGGTC 57.909 45.455 0.86 0.00 33.81 3.85
3330 3868 5.940617 TGGCTTCAAGGTATGCATAACTAT 58.059 37.500 24.30 11.89 28.28 2.12
3402 3941 2.234661 GCCTGCTGCTTCCCTTAAAATT 59.765 45.455 0.00 0.00 36.87 1.82
3427 3966 7.335627 TGCCCCATGCTATATTTACATACTAC 58.664 38.462 0.00 0.00 42.00 2.73
3480 4064 4.843220 AACCTGCAAAAGATCTGAAGTG 57.157 40.909 0.00 0.00 0.00 3.16
3497 4081 6.815641 TCTGAAGTGAGAACAAAGATATGCTC 59.184 38.462 0.00 0.00 0.00 4.26
3571 4155 3.366052 AACACTTCTTTGACCACCAGT 57.634 42.857 0.00 0.00 0.00 4.00
3624 4208 8.492673 TTTCTTTCTTTCAGTGTATGCGATAT 57.507 30.769 0.00 0.00 0.00 1.63
3625 4209 7.468922 TCTTTCTTTCAGTGTATGCGATATG 57.531 36.000 0.00 0.00 0.00 1.78
3657 4250 8.299570 AGTATCAATGCACTCTTAACTTTTTGG 58.700 33.333 0.00 0.00 0.00 3.28
3674 4267 0.178967 TGGCTGCAATTCCCAGAACA 60.179 50.000 0.50 2.85 32.03 3.18
3689 4282 3.859386 CCAGAACACTTGTTTCTGTTTGC 59.141 43.478 10.38 0.00 38.56 3.68
3760 4354 9.003658 AGTATATTGCTTAATGATACTGCCAAC 57.996 33.333 0.00 0.00 33.21 3.77
3890 4542 6.477033 TCTTAGCTCTGACTATTGAAATTCGC 59.523 38.462 0.00 0.00 0.00 4.70
3910 4562 2.552155 GCCCCTACAACATTCTGACACA 60.552 50.000 0.00 0.00 0.00 3.72
3957 4611 9.803315 GGGGAATTTTTAATCTATTGAACTGTC 57.197 33.333 0.00 0.00 0.00 3.51
3990 4647 3.759581 AGACATGCTGGAGTCAAATTGT 58.240 40.909 0.00 0.00 37.23 2.71
3991 4648 4.910195 AGACATGCTGGAGTCAAATTGTA 58.090 39.130 0.00 0.00 37.23 2.41
4061 4718 3.667360 TGTCATTATCATCGAGGGCATG 58.333 45.455 0.00 0.00 0.00 4.06
4068 4725 1.228063 ATCGAGGGCATGATGGTGC 60.228 57.895 0.00 0.00 44.31 5.01
4108 4765 4.641989 ATGACAGTTCAACCATTATCTGGC 59.358 41.667 0.00 0.00 40.35 4.85
4253 4910 4.706616 AGGGGAGGAATAGTTAACTTCCA 58.293 43.478 22.64 4.33 42.83 3.53
4326 4984 7.418254 GCTTAAATGAAGAACCCATCCATTCAT 60.418 37.037 0.00 0.00 41.18 2.57
4329 4987 7.534723 AATGAAGAACCCATCCATTCATATG 57.465 36.000 0.00 0.00 39.13 1.78
4388 5071 5.774179 ACCTGTACTGGACTAGCCTAAATA 58.226 41.667 24.19 0.00 37.63 1.40
4391 5074 6.493802 CCTGTACTGGACTAGCCTAAATATCA 59.506 42.308 13.30 0.00 37.63 2.15
4394 5077 9.769677 TGTACTGGACTAGCCTAAATATCATAT 57.230 33.333 0.00 0.00 37.63 1.78
4481 5168 6.459298 GGCCATGAGTTCTTTCTTGATGTATG 60.459 42.308 0.00 0.00 0.00 2.39
4530 5219 5.168569 TCAGCTAACCTTCAGTTATTGTCG 58.831 41.667 0.00 0.00 40.18 4.35
4576 5265 2.257409 GAGGATGGTGACGGTGGCAT 62.257 60.000 0.00 0.00 0.00 4.40
4610 5299 0.877071 AAGCTGTGGTCTCATTTGCG 59.123 50.000 0.00 0.00 0.00 4.85
4778 5467 9.991388 TGTAATGTATTATTGTTTTTCTACCGC 57.009 29.630 0.00 0.00 0.00 5.68
4834 5523 3.297134 TGAAACTGTTGCTCCTCCTTT 57.703 42.857 0.00 0.00 0.00 3.11
5045 5737 4.829064 TGTTGTAGTTGCTGTTCCATTC 57.171 40.909 0.00 0.00 0.00 2.67
5070 5762 4.777896 ACTGTGTGTCTGAATATACCAGGT 59.222 41.667 0.00 0.00 32.73 4.00
5115 5807 4.389077 GTGGGAATGTAAGTTTCTCTGTCG 59.611 45.833 0.00 0.00 0.00 4.35
5196 5888 5.895928 TCTGTTTCGATAACAGGAGATGAG 58.104 41.667 26.05 10.63 45.66 2.90
5280 5972 3.499918 AGGTTCTGTCGAAAAGATTGCAG 59.500 43.478 0.23 0.00 0.00 4.41
5368 6060 0.040067 GAATCCGATTCGCCATTGCC 60.040 55.000 5.36 0.00 0.00 4.52
5441 6133 2.795231 CATCCACATCACTGGAGGTT 57.205 50.000 0.00 0.00 43.82 3.50
5519 6211 1.130561 CGACAAAAATTCGAGGGCCTC 59.869 52.381 24.06 24.06 38.85 4.70
5530 6222 0.110486 GAGGGCCTCTTTGGTTCACA 59.890 55.000 26.44 0.00 38.35 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.201696 GCCTGCAAAAATTCATCATGAAATCAT 60.202 33.333 3.63 0.00 40.12 2.45
1 2 6.092944 GCCTGCAAAAATTCATCATGAAATCA 59.907 34.615 3.63 0.00 40.12 2.57
2 3 6.092944 TGCCTGCAAAAATTCATCATGAAATC 59.907 34.615 3.63 0.00 40.12 2.17
3 4 5.941058 TGCCTGCAAAAATTCATCATGAAAT 59.059 32.000 3.63 0.00 40.12 2.17
4 5 5.179742 GTGCCTGCAAAAATTCATCATGAAA 59.820 36.000 3.63 0.00 40.12 2.69
5 6 4.691685 GTGCCTGCAAAAATTCATCATGAA 59.308 37.500 1.59 1.59 41.09 2.57
6 7 4.020928 AGTGCCTGCAAAAATTCATCATGA 60.021 37.500 0.00 0.00 0.00 3.07
7 8 4.250464 AGTGCCTGCAAAAATTCATCATG 58.750 39.130 0.00 0.00 0.00 3.07
8 9 4.546829 AGTGCCTGCAAAAATTCATCAT 57.453 36.364 0.00 0.00 0.00 2.45
9 10 4.339872 AAGTGCCTGCAAAAATTCATCA 57.660 36.364 0.00 0.00 0.00 3.07
10 11 5.713025 TCTAAGTGCCTGCAAAAATTCATC 58.287 37.500 0.00 0.00 0.00 2.92
11 12 5.726980 TCTAAGTGCCTGCAAAAATTCAT 57.273 34.783 0.00 0.00 0.00 2.57
12 13 5.068987 AGTTCTAAGTGCCTGCAAAAATTCA 59.931 36.000 0.00 0.00 0.00 2.57
13 14 5.532557 AGTTCTAAGTGCCTGCAAAAATTC 58.467 37.500 0.00 0.00 0.00 2.17
14 15 5.535753 AGTTCTAAGTGCCTGCAAAAATT 57.464 34.783 0.00 0.00 0.00 1.82
15 16 5.535753 AAGTTCTAAGTGCCTGCAAAAAT 57.464 34.783 0.00 0.00 0.00 1.82
16 17 5.337578 AAAGTTCTAAGTGCCTGCAAAAA 57.662 34.783 0.00 0.00 0.00 1.94
17 18 5.108517 CAAAAGTTCTAAGTGCCTGCAAAA 58.891 37.500 0.00 0.00 0.00 2.44
18 19 4.159506 ACAAAAGTTCTAAGTGCCTGCAAA 59.840 37.500 0.00 0.00 0.00 3.68
19 20 3.699038 ACAAAAGTTCTAAGTGCCTGCAA 59.301 39.130 0.00 0.00 0.00 4.08
20 21 3.287222 ACAAAAGTTCTAAGTGCCTGCA 58.713 40.909 0.00 0.00 0.00 4.41
21 22 3.315191 TGACAAAAGTTCTAAGTGCCTGC 59.685 43.478 0.00 0.00 0.00 4.85
22 23 5.499139 TTGACAAAAGTTCTAAGTGCCTG 57.501 39.130 0.00 0.00 0.00 4.85
23 24 5.594317 ACATTGACAAAAGTTCTAAGTGCCT 59.406 36.000 0.00 0.00 0.00 4.75
24 25 5.831997 ACATTGACAAAAGTTCTAAGTGCC 58.168 37.500 0.00 0.00 0.00 5.01
25 26 7.702348 AGAAACATTGACAAAAGTTCTAAGTGC 59.298 33.333 9.09 0.00 0.00 4.40
26 27 9.226345 GAGAAACATTGACAAAAGTTCTAAGTG 57.774 33.333 9.09 0.00 0.00 3.16
27 28 9.178758 AGAGAAACATTGACAAAAGTTCTAAGT 57.821 29.630 9.09 0.00 0.00 2.24
28 29 9.657121 GAGAGAAACATTGACAAAAGTTCTAAG 57.343 33.333 9.09 0.00 0.00 2.18
29 30 9.173021 TGAGAGAAACATTGACAAAAGTTCTAA 57.827 29.630 9.09 0.00 0.00 2.10
30 31 8.731275 TGAGAGAAACATTGACAAAAGTTCTA 57.269 30.769 9.09 0.00 0.00 2.10
31 32 7.630242 TGAGAGAAACATTGACAAAAGTTCT 57.370 32.000 9.09 9.17 0.00 3.01
32 33 8.687824 TTTGAGAGAAACATTGACAAAAGTTC 57.312 30.769 9.09 5.33 0.00 3.01
33 34 9.487790 TTTTTGAGAGAAACATTGACAAAAGTT 57.512 25.926 0.00 0.00 37.18 2.66
79 80 6.360844 TCGGTGAACAGTAAAATCGAAAAA 57.639 33.333 0.00 0.00 0.00 1.94
80 81 5.559417 GCTCGGTGAACAGTAAAATCGAAAA 60.559 40.000 0.00 0.00 0.00 2.29
81 82 4.084223 GCTCGGTGAACAGTAAAATCGAAA 60.084 41.667 0.00 0.00 0.00 3.46
82 83 3.430895 GCTCGGTGAACAGTAAAATCGAA 59.569 43.478 0.00 0.00 0.00 3.71
83 84 2.991190 GCTCGGTGAACAGTAAAATCGA 59.009 45.455 0.00 0.00 0.00 3.59
84 85 2.993899 AGCTCGGTGAACAGTAAAATCG 59.006 45.455 0.00 0.00 0.00 3.34
85 86 3.994392 TGAGCTCGGTGAACAGTAAAATC 59.006 43.478 9.64 0.00 0.00 2.17
86 87 4.002906 TGAGCTCGGTGAACAGTAAAAT 57.997 40.909 9.64 0.00 0.00 1.82
87 88 3.462483 TGAGCTCGGTGAACAGTAAAA 57.538 42.857 9.64 0.00 0.00 1.52
88 89 3.462483 TTGAGCTCGGTGAACAGTAAA 57.538 42.857 9.64 0.00 0.00 2.01
89 90 3.462483 TTTGAGCTCGGTGAACAGTAA 57.538 42.857 9.64 0.00 0.00 2.24
90 91 3.006430 TCATTTGAGCTCGGTGAACAGTA 59.994 43.478 9.64 0.00 0.00 2.74
91 92 2.146342 CATTTGAGCTCGGTGAACAGT 58.854 47.619 9.64 0.00 0.00 3.55
92 93 2.414481 CTCATTTGAGCTCGGTGAACAG 59.586 50.000 9.64 0.00 35.13 3.16
93 94 2.416747 CTCATTTGAGCTCGGTGAACA 58.583 47.619 9.64 0.00 35.13 3.18
114 115 1.743252 GTGCCTTTCTGCTCCCGAG 60.743 63.158 0.00 0.00 0.00 4.63
115 116 1.768684 AAGTGCCTTTCTGCTCCCGA 61.769 55.000 0.00 0.00 0.00 5.14
116 117 0.890996 AAAGTGCCTTTCTGCTCCCG 60.891 55.000 0.00 0.00 0.00 5.14
117 118 0.884514 GAAAGTGCCTTTCTGCTCCC 59.115 55.000 16.08 0.00 44.33 4.30
118 119 0.519077 CGAAAGTGCCTTTCTGCTCC 59.481 55.000 19.11 1.19 45.19 4.70
119 120 0.519077 CCGAAAGTGCCTTTCTGCTC 59.481 55.000 19.11 0.00 45.19 4.26
120 121 0.890996 CCCGAAAGTGCCTTTCTGCT 60.891 55.000 19.11 0.00 45.19 4.24
121 122 0.889186 TCCCGAAAGTGCCTTTCTGC 60.889 55.000 19.11 0.00 45.19 4.26
122 123 1.470098 CATCCCGAAAGTGCCTTTCTG 59.530 52.381 19.11 14.69 45.19 3.02
123 124 1.351017 TCATCCCGAAAGTGCCTTTCT 59.649 47.619 19.11 4.59 45.19 2.52
124 125 1.821216 TCATCCCGAAAGTGCCTTTC 58.179 50.000 14.28 14.28 44.29 2.62
125 126 2.094675 CATCATCCCGAAAGTGCCTTT 58.905 47.619 0.46 0.46 36.29 3.11
126 127 1.281867 TCATCATCCCGAAAGTGCCTT 59.718 47.619 0.00 0.00 0.00 4.35
127 128 0.911769 TCATCATCCCGAAAGTGCCT 59.088 50.000 0.00 0.00 0.00 4.75
128 129 1.017387 GTCATCATCCCGAAAGTGCC 58.983 55.000 0.00 0.00 0.00 5.01
129 130 1.737838 TGTCATCATCCCGAAAGTGC 58.262 50.000 0.00 0.00 0.00 4.40
130 131 4.970662 ATTTGTCATCATCCCGAAAGTG 57.029 40.909 0.00 0.00 0.00 3.16
131 132 5.989477 TCTATTTGTCATCATCCCGAAAGT 58.011 37.500 0.00 0.00 0.00 2.66
132 133 5.049818 GCTCTATTTGTCATCATCCCGAAAG 60.050 44.000 0.00 0.00 0.00 2.62
133 134 4.816385 GCTCTATTTGTCATCATCCCGAAA 59.184 41.667 0.00 0.00 0.00 3.46
134 135 4.141733 TGCTCTATTTGTCATCATCCCGAA 60.142 41.667 0.00 0.00 0.00 4.30
135 136 3.387699 TGCTCTATTTGTCATCATCCCGA 59.612 43.478 0.00 0.00 0.00 5.14
136 137 3.732212 TGCTCTATTTGTCATCATCCCG 58.268 45.455 0.00 0.00 0.00 5.14
225 243 4.141482 GGTGGAGGTATTTATTGAGCTGGA 60.141 45.833 0.00 0.00 0.00 3.86
280 313 3.142787 TGGAGGGATGGTAGATGATGAGA 59.857 47.826 0.00 0.00 0.00 3.27
291 324 3.165071 GTGATGTTTTTGGAGGGATGGT 58.835 45.455 0.00 0.00 0.00 3.55
366 403 1.863155 TTGGCTCCCCCATGTCCTTC 61.863 60.000 0.00 0.00 44.89 3.46
385 422 2.418609 GGGTTGTTTCTGCAAAGTGCTT 60.419 45.455 1.43 0.00 45.31 3.91
387 424 1.570813 GGGTTGTTTCTGCAAAGTGC 58.429 50.000 0.00 0.00 45.29 4.40
397 434 1.407618 GGACAGTGTTGGGGTTGTTTC 59.592 52.381 0.00 0.00 0.00 2.78
409 446 2.329267 TGGAGATCACAAGGACAGTGT 58.671 47.619 0.00 0.00 38.16 3.55
552 979 5.030147 TCTCTCTCTCTACCTCTCTCTGTT 58.970 45.833 0.00 0.00 0.00 3.16
585 1012 2.781406 GGTCTCCTCTCCCACCCT 59.219 66.667 0.00 0.00 0.00 4.34
586 1013 2.365768 GGGTCTCCTCTCCCACCC 60.366 72.222 0.00 0.00 42.95 4.61
668 1095 0.254747 CTGGTCTCGTCTCCTCTCCT 59.745 60.000 0.00 0.00 0.00 3.69
669 1096 1.381165 GCTGGTCTCGTCTCCTCTCC 61.381 65.000 0.00 0.00 0.00 3.71
810 1243 1.156645 GGGCTCGTGATGATCACTGC 61.157 60.000 21.83 22.43 44.85 4.40
948 1395 0.872388 ACGGCGGCAGTTAAAAGAAG 59.128 50.000 13.24 0.00 0.00 2.85
950 1397 0.589223 CAACGGCGGCAGTTAAAAGA 59.411 50.000 17.74 0.00 0.00 2.52
989 1439 1.821061 CGGATCCATCCCCTTCTCCG 61.821 65.000 13.41 0.00 44.24 4.63
1206 1659 2.124693 GGCACGGGGAGAGAGAGAG 61.125 68.421 0.00 0.00 0.00 3.20
1251 1707 1.226603 GACCAACGAGACCGATCCG 60.227 63.158 0.00 0.00 39.50 4.18
1264 1720 2.735478 CTACCGCGCGTTGACCAA 60.735 61.111 29.95 0.00 0.00 3.67
1325 1781 2.290916 GCAGACGATGAATCTCTACCGA 59.709 50.000 0.00 0.00 0.00 4.69
1363 1819 7.786178 TTCATCCCAATTAGTACTGAAATCG 57.214 36.000 5.39 0.00 0.00 3.34
1372 1828 8.160765 TCAAAGTGAGTTTCATCCCAATTAGTA 58.839 33.333 0.00 0.00 0.00 1.82
1603 2120 3.795688 TCTGGCCTTTTGTCAGATTCT 57.204 42.857 3.32 0.00 33.21 2.40
1631 2148 4.462483 GCTTTCCATTATGAACAGAACCCA 59.538 41.667 0.00 0.00 0.00 4.51
1822 2343 8.036575 AGCTGTGCACAATGATAAACAAAATAT 58.963 29.630 21.98 0.00 0.00 1.28
1921 2458 4.761739 ACATACTGCTTTACAACTGTGCAT 59.238 37.500 0.00 0.00 33.02 3.96
1943 2480 4.437255 CCAAAGCAAGCCTTTTGTTTGAAC 60.437 41.667 12.30 0.00 41.75 3.18
1979 2516 1.111715 GGATGCCAATTCTCCAGCCC 61.112 60.000 0.00 0.00 0.00 5.19
2010 2547 6.214191 ACCATCCGATGCTCTTATATACTG 57.786 41.667 2.53 0.00 0.00 2.74
2012 2549 7.773149 ACTAACCATCCGATGCTCTTATATAC 58.227 38.462 2.53 0.00 0.00 1.47
2013 2550 7.956328 ACTAACCATCCGATGCTCTTATATA 57.044 36.000 2.53 0.00 0.00 0.86
2015 2552 6.041637 ACAACTAACCATCCGATGCTCTTATA 59.958 38.462 2.53 0.00 0.00 0.98
2017 2554 4.161565 ACAACTAACCATCCGATGCTCTTA 59.838 41.667 2.53 0.00 0.00 2.10
2018 2555 3.055094 ACAACTAACCATCCGATGCTCTT 60.055 43.478 2.53 0.00 0.00 2.85
2019 2556 2.501723 ACAACTAACCATCCGATGCTCT 59.498 45.455 2.53 0.00 0.00 4.09
2020 2557 2.906354 ACAACTAACCATCCGATGCTC 58.094 47.619 2.53 0.00 0.00 4.26
2021 2558 3.270877 GAACAACTAACCATCCGATGCT 58.729 45.455 2.53 0.00 0.00 3.79
2022 2559 3.006940 TGAACAACTAACCATCCGATGC 58.993 45.455 2.53 0.00 0.00 3.91
2023 2560 3.063997 GCTGAACAACTAACCATCCGATG 59.936 47.826 0.93 0.93 0.00 3.84
2541 3079 5.819825 AATCGCCCAAGAAAAGATAGTTC 57.180 39.130 0.00 0.00 0.00 3.01
2794 3332 5.376625 GGAAAGACCTCCATGCATACATAA 58.623 41.667 0.00 0.00 35.36 1.90
2925 3463 1.922447 TCATTCATAGCCCACCCTTGT 59.078 47.619 0.00 0.00 0.00 3.16
3124 3662 0.456221 ACTCGTAGCCATCCTCAACG 59.544 55.000 0.00 0.00 34.99 4.10
3330 3868 5.486526 GCAAAATACCAATTGTTCCCATGA 58.513 37.500 4.43 0.00 0.00 3.07
3381 3919 1.256812 TTTTAAGGGAAGCAGCAGGC 58.743 50.000 0.00 0.00 45.30 4.85
3389 3927 3.682436 GCATGGGGCAATTTTAAGGGAAG 60.682 47.826 0.00 0.00 43.97 3.46
3480 4064 6.054295 ACTCCATGAGCATATCTTTGTTCTC 58.946 40.000 0.00 0.00 32.04 2.87
3497 4081 2.981898 TCTGCAGTGAATGACTCCATG 58.018 47.619 14.67 0.00 32.36 3.66
3550 4134 4.497291 ACTGGTGGTCAAAGAAGTGTTA 57.503 40.909 0.00 0.00 0.00 2.41
3571 4155 2.334946 GCATCTGCGGTTCTGGCAA 61.335 57.895 0.00 0.00 40.39 4.52
3624 4208 3.321968 AGAGTGCATTGATACTATCGCCA 59.678 43.478 0.00 0.00 0.00 5.69
3625 4209 3.919216 AGAGTGCATTGATACTATCGCC 58.081 45.455 0.00 0.00 0.00 5.54
3657 4250 1.251251 AGTGTTCTGGGAATTGCAGC 58.749 50.000 0.00 0.00 0.00 5.25
3674 4267 4.729868 AGATAGGGCAAACAGAAACAAGT 58.270 39.130 0.00 0.00 0.00 3.16
3689 4282 1.770658 TCAAGTGCATGGGAGATAGGG 59.229 52.381 0.00 0.00 0.00 3.53
3767 4361 5.901552 AGTTAACACATTTGGTTGACTTGG 58.098 37.500 8.61 0.00 40.77 3.61
3890 4542 3.244561 ACTGTGTCAGAATGTTGTAGGGG 60.245 47.826 3.70 0.00 37.40 4.79
3910 4562 6.159751 TCCCCAGGAGTAAATAAAGCATTACT 59.840 38.462 0.00 0.00 43.22 2.24
3990 4647 7.442666 TGCAATATGCTTACACGTATTCCAATA 59.557 33.333 3.78 0.00 45.31 1.90
3991 4648 6.262049 TGCAATATGCTTACACGTATTCCAAT 59.738 34.615 3.78 0.00 45.31 3.16
4061 4718 3.118629 TGAGGTCAATGTCTAGCACCATC 60.119 47.826 0.00 0.00 0.00 3.51
4068 4725 5.077134 TGTCATGTGAGGTCAATGTCTAG 57.923 43.478 0.00 0.00 0.00 2.43
4108 4765 4.809426 AGAAAGAAATGGCGGTAGATAACG 59.191 41.667 0.00 0.00 0.00 3.18
4122 4779 8.230486 GACACAATGTCATCGTAAGAAAGAAAT 58.770 33.333 4.08 0.00 46.22 2.17
4326 4984 4.299586 TGGGATGTTGCTTGTTCTCATA 57.700 40.909 0.00 0.00 0.00 2.15
4329 4987 2.165030 CCATGGGATGTTGCTTGTTCTC 59.835 50.000 2.85 0.00 0.00 2.87
4355 5038 5.273208 AGTCCAGTACAGGTTCATAGATGT 58.727 41.667 3.99 0.00 0.00 3.06
4415 5099 3.459232 TCATACAGCTAGTGGCATGTC 57.541 47.619 0.00 0.00 44.79 3.06
4426 5113 7.831193 ACAACTGAGGATTATTTTCATACAGCT 59.169 33.333 0.00 0.00 0.00 4.24
4481 5168 7.047460 ACATCAAAAGAGCCCATTATCATTC 57.953 36.000 0.00 0.00 0.00 2.67
4576 5265 2.334946 GCTTGCTCACCAATCGCCA 61.335 57.895 0.00 0.00 31.91 5.69
4778 5467 2.096565 TCGTACGATAAAGAGATCCGCG 60.097 50.000 15.28 0.00 0.00 6.46
5045 5737 5.582269 CCTGGTATATTCAGACACACAGTTG 59.418 44.000 7.39 0.00 34.36 3.16
5070 5762 1.926665 AGGCCACCACCCAATAACATA 59.073 47.619 5.01 0.00 0.00 2.29
5115 5807 4.760715 CCAGGATCAAGATGTCATGATTCC 59.239 45.833 0.00 5.74 34.82 3.01
5196 5888 7.725251 AGACATATTCTCTTCATCTCCACTTC 58.275 38.462 0.00 0.00 0.00 3.01
5368 6060 2.046507 GGCTGAGTGAGGCCTGTG 60.047 66.667 12.00 0.00 44.48 3.66
5407 6099 6.543465 TGATGTGGATGTGTCTATTCCAATTC 59.457 38.462 0.00 0.00 41.05 2.17
5441 6133 5.971202 GCAGAAAATCGTTCTTGTTTCTTCA 59.029 36.000 0.00 0.00 38.05 3.02
5519 6211 6.473455 GTGTTCTGAATTTCTGTGAACCAAAG 59.527 38.462 18.33 0.00 36.98 2.77
5530 6222 6.861065 ATGTGTAACGTGTTCTGAATTTCT 57.139 33.333 0.00 0.00 42.39 2.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.